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1500 questions
4
votes
4 answers
What are the standard ways to visualize protein-protein or gene-gene interactions?
I would like to visualize this interaction list. Is there an online/web based way to do it? Is there a way to analyze the data?
Assuming I have exported the list into lines such as:
2 A2M 348 APOE
0x90
- 1,437
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4
votes
1 answer
How can I combine a kinship matrix with subset individuals when using rvtests?
I've been processing data for a consortium project that uses the rvtests toolkit. Our data analysis process uses a kinship matrix and the calculation of inverse-normalised transformed statistics after covariate adjustment (for 1kG-imputed data from…
gringer
- 14,012
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- 79
4
votes
1 answer
How to calculate Fst from AMOVA
I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping factor and "Error")
I have two questions:
What does…
Beatrice Baldi
- 43
- 4
4
votes
3 answers
mrbayes, Sumt ; Error when setting parameter "Filename" (1)
question 1
I wanted to use sumt command after completion of mcmc run. Whenever I use, sumt Filename=infile.nex, it gives me the error:
A matrix must be specified before sumt can be used
Error when setting parameter "Filename" (1)
But for the same…
zillur rahman
- 307
- 2
- 13
4
votes
1 answer
How can I identify a recessive and dominant gene?
For example, I have two allelic genes. How can I identify a recessive and dominant gene? Are there any databases with this information? Or the answer to my question is to study the concept of "haplosufficiency"?
Элл Нейгебауэр
- 43
- 2
4
votes
2 answers
Mapping Reads to Known Gene Paralogs with Long Read Technology
I have some sequencing data from a captured region that is a known paralog edited. For now, I have been mapping the data using standard minimap2 flags for PacBio DNA sequencing:
minimap2 -ax map-pb GRCh37.fa fastqfile.fastq > samfile.sam
I captured…
d_kennetz
- 631
- 5
- 17
4
votes
1 answer
How to plot p-values in a circular barplot?
Im trying to plot reactome pathway in for of circular bar plot using ggplot2
my data
dput(df2)
structure(list(ID = 1:10, Pathway_names = structure(c(5L, 1L,
7L, 6L, 2L, 3L, 9L, 8L, 10L, 4L), .Label = c("Antigen Presentation: Folding assembly…
kcm
- 1,804
- 12
- 27
4
votes
1 answer
Snakemake: Cannot find first rule?
Back again with another snakemake query. This time I decided to port my read cleaning and alignment pipeline to snakemake. Repeating the steps from previous question and trying not to make any typo here, I'm now receiving this "error" while trying a…
Siddharth
- 345
- 2
- 12
4
votes
2 answers
Extracting all reads from bam file which match read IDs in another file
I have a long list of read IDs of interest to me in a file called read_names.txt. it is simply in the format:
m54197_180831_211346/4981510/ccs
m54197_180831_211346/6226723/ccs
m54197_180831_211346/6619607/ccs
...
etc where these are the actual read…
d_kennetz
- 631
- 5
- 17
4
votes
1 answer
Parsing gtf file for transcript ID and transcript name
I used this previously to get ensembl ID and its gene name from the gencode gtf annotation file
This was the script I used
awk '{
for (i = 1; i <= NF; i++) {
if ($i ~ /gene_id|gene_name/) {
…
kcm
- 1,804
- 12
- 27
4
votes
1 answer
How to find genomic overlaps faster?
I was trying to find a way to find overlaps between two genomic ranges. I found a post at Biostars but it couldn't consider the chromosome information. For example:
library(IRanges)
df1 = data.frame(chr = c("chr1", "chr12"), start = c(10000, 10000),…
satyanarayan rao
- 79
- 4
4
votes
1 answer
How should I address batch effects in my experiment?
Let's say I have an RNA-Seq experiment, where I'm interested in the significantly differentiated genes between pre-treatment and post-treatment conditions. "rep" == biological replicate.
Sample PreA (3 reps **all** in 2017) vs Sample PostA (3 reps…
SmallChess
- 2,699
- 3
- 19
- 35
4
votes
1 answer
What are 2D reads in the Oxford MinIon?
Reading the Mash: fast genome and metagenome distance estimation paper, I see the reference to "2d reads" notion under the minION context (a sequencing technique)
e.g
In both cases Mash was able to
correctly differentiate these closely related…
DsCpp
- 143
- 4
4
votes
5 answers
Fast and reliable alternatives to blast
After some unexpected results (and previously reported) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate.
I only found hmmer, but I don't know if it is faster and more accurate.
Is…
llrs
- 4,693
- 1
- 18
- 42
4
votes
1 answer
Simulate and test CNV workflow?
I'd like to evaluate a CNV project.
My aim is to evaluate if the scripts are sufficient for calling reasonable CNVs. I know they have a paper, but their scripts may be buggy... and all papers are biased...
While there are CNV simulators on Google…
SmallChess
- 2,699
- 3
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- 35